Download or read book Strategies for the Structure Based Analysis of Protein Functionality written by Aysam Gürler and published by . This book was released on 2009 with total page 39 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Molecular Biology of the Cell written by and published by . This book was released on 2002 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Protein Structure Analysis written by Roza Maria Kamp and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 311 pages. Available in PDF, EPUB and Kindle. Book excerpt: "Protein Structure Analysis - Preparation and Characterization" is a compilation of practical approaches to the structural analysis of proteins and peptides. Here, about 20 authors describe and comment on techniques for sensitive protein purification and analysis. These methods are used worldwide in biochemical and biotechnical research currently being carried out in pharmaceu tical and biomedical laboratories or protein sequencing facilities. The chapters have been written by scientists with extensive ex perience in these fields, and the practical parts are well documen ted so that the reader should be able to easily reproduce the described techniques. The methods compiled in this book were demonstrated in student courses and in the EMBO Practical Course on "Microsequence Analysis of Proteins" held in Berlin September 10-15, 1995. The topics also derived from a FEBS Workshop, held in Halkidiki, Thessaloniki, Greece, in April, 1995. Most of the authors participated in these courses as lecturers and tutors and made these courses extremely lively and successful. Since polypeptides greatly vary depending on their specific structure and function, strategies for their structural analysis must for the most part be adapted to each individual protein. Therefore, advantages and limitations of the experimen tal approaches are discussed here critically, so that the reader becomes familiar with problems that might be encountered.

Download or read book Protein Structure written by Daniel Chasman and published by CRC Press. This book was released on 2003-03-18 with total page 534 pages. Available in PDF, EPUB and Kindle. Book excerpt: This text offers in-depth perspectives on every aspect of protein structure identification, assessment, characterization, and utilization, for a clear understanding of the diversity of protein shapes, variations in protein function, and structure-based drug design. The authors cover numerous high-throughput technologies as well as computational methods to study protein structures and residues. A valuable reference, this book reflects current trends in the effort to solve new structures arising from genome initiatives, details methods to detect and identify errors in the prediction of protein structural models, and outlines challenges in the conversion of routine processes into high-throughput platforms.

Download or read book Protein Function Prediction Methods and Protocols written by Daisuke Kihara and published by Methods in Molecular Biology. This book was released on 2019-05-12 with total page 252 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book From Protein Structure to Function with Bioinformatics written by Daniel John Rigden and published by Springer Science & Business Media. This book was released on 2008-12-11 with total page 330 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins lie at the heart of almost all biological processes and have an incredibly wide range of activities. Central to the function of all proteins is their ability to adopt, stably or sometimes transiently, structures that allow for interaction with other molecules. An understanding of the structure of a protein can therefore lead us to a much improved picture of its molecular function. This realisation has been a prime motivation of recent Structural Genomics projects, involving large-scale experimental determination of protein structures, often those of proteins about which little is known of function. These initiatives have, in turn, stimulated the massive development of novel methods for prediction of protein function from structure. Since model structures may also take advantage of new function prediction algorithms, the first part of the book deals with the various ways in which protein structures may be predicted or inferred, including specific treatment of membrane and intrinsically disordered proteins. A detailed consideration of current structure-based function prediction methodologies forms the second part of this book, which concludes with two chapters, focusing specifically on case studies, designed to illustrate the real-world application of these methods. With bang up-to-date texts from world experts, and abundant links to publicly available resources, this book will be invaluable to anyone who studies proteins and the endlessly fascinating relationship between their structure and function.

Download or read book Protein Engineering Protocols written by Kristian Müller and published by Springer Science & Business Media. This book was released on 2007-10-26 with total page 318 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein engineering is a fascinating mixture of molecular biology, protein structure analysis, computation, and biochemistry, with the goal of developing useful or valuable proteins. Protein Engineering Protocols will consider the two general, but not mutually exclusive, strategies for protein engineering. The first is known as rational design, in which the scientist uses detailed knowledge of the structure and function of the protein to make desired changes. The s- ond strategy is known as directed evolution. In this case, random mutagenesis is applied to a protein, and selection or screening is used to pick out variants that have the desired qualities. By several rounds of mutation and selection, this method mimics natural evolution. An additional technique known as DNA shuffling mixes and matches pieces of successful variants to produce better results. This process mimics recombination that occurs naturally during sexual reproduction. The first section of Protein Engineering Protocols describes rational p- tein design strategies, including computational methods, the use of non-natural amino acids to expand the biological alphabet, as well as impressive examples for the generation of proteins with novel characteristics. Although procedures for the introduction of mutations have become routine, predicting and und- standing the effects of these mutations can be very challenging and requires profound knowledge of the system as well as protein structures in general.

Download or read book Complementary Strategies to Study Virus Structure and Function written by and published by Academic Press. This book was released on 2019-09-13 with total page 352 pages. Available in PDF, EPUB and Kindle. Book excerpt: Complementary Strategies to Study Virus Structure and Function, Volume 104, the latest release in the Advances in Virus Research series, highlights new advances in the field, with this new volume presenting interesting chapters on X-ray structures from crystals of viral proteins grown in cellula, NMR and SAXS to study protein dynamics and natively disordered viral proteins, Mass spectrometry to study virus particle assembly, Atomic force microscopy to study virus particles, Non-enveloped viruses and interactions with antibodies, Non-enveloped viruses and their mechanism of entry into cells, Structures of enveloped virions by electron cryo-microscopy and cryo-tomography, and many other interesting topics. - Provides the authority and expertise of leading contributors from an international board of authors - Presents the latest release in the Advances in Virus Research series - Includes the latest information on virus structure and function

Download or read book Protein Structure Stability and Folding written by Kenneth P. Murphy and published by Springer Science & Business Media. This book was released on 2008-02-04 with total page 258 pages. Available in PDF, EPUB and Kindle. Book excerpt: In Protein Structure, Stability, and Folding, Kenneth P. Murphy and a panel of internationally recognized investigators describe some of the newest experimental and theoretical methods for investigating these critical events and processes. Among the techniques discussed are the many methods for calculating many of protein stability and dynamics from knowledge of the structure, and for performing molecular dynamics simulations of protein unfolding. New experimental approaches presented include the use of co-solvents, novel applications of hydrogen exchange techniques, temperature-jump methods for looking at folding events, and new strategies for mutagenesis experiments. Unique in its powerful combination of theory and practice, Protein Structure, Stability, and Folding offers protein and biophysical chemists the means to gain a more comprehensive understanding of some of this complex area by detailing many of the major techniques in use today.

Download or read book Computational Protein Design written by Ilan Samish and published by Humana. This book was released on 2016-12-03 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The aim this volume is to present the methods, challenges, software, and applications of this widespread and yet still evolving and maturing field. Computational Protein Design, the first book with this title, guides readers through computational protein design approaches, software and tailored solutions to specific case-study targets. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Computational Protein Design aims to ensure successful results in the further study of this vital field.

Download or read book Toward an Automated Strategy for Superfamily Analysis and Characterization of Proteins written by Shoshana Brown and published by . This book was released on 2005 with total page 468 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational methods for protein function prediction are required to bridge the gap between the number of sequenced genes and the number of experimentally characterized proteins. In this thesis I present a new framework for the organization of protein sequence, structure, and functional information that facilitates computational function prediction. In Chapter II present a semi-automated method for the collection and functional annotation of human transporter genes. Annotation of these genes is performed by placing them within the context of a characterized family, and leveraging existing information about family-specific structure-function relationships to infer their function, in a preliminary application of the Superfamily analysis method that is further explored in subsequent chapters. Streamlining the Superfamily analysis strategy requires a platform that presents Superfamily structure-function data in an easily accessible format. Chapter II describes the development of a Structure-Function Linkage Database (SFLD) to fulfill this purpose. The issues involved in database design are discussed, and an overview of the database functionality is given. The use of the database to address several types of real scientific problems is discussed. Without data, the SFLD schema is of limited use to the research community. Chapter III describes the development of a set of gold standard superfamilies that provide a preliminary dataset for the SFLD and a test set for automated methods that aim to cluster proteins based on sequence, structure, and function. The properties differentiating the gold standard set from existing datasets, as well as the difficulties involved in clustering enzymes in mechanistically diverse superfamilies are discussed. The SFLD may be used for several different purposes. Chapter IV presents two detailed scenarios for using the SFLD--the functional annotation of an uncharacterized protein and analysis of a previously annotated protein to detect misannotation. Chapter V presents some additional contributions that I have made to the SFLD. Development of the database schema is discussed in terms of the requirements for representing structure-function relationships in mechanistically diverse enzyme superfamilies. The automated update protocol for the SFLD is also presented.

Download or read book Analytical Techniques for the Elucidation of Protein Function written by Isao Suetake and published by John Wiley & Sons. This book was released on 2023-01-04 with total page 245 pages. Available in PDF, EPUB and Kindle. Book excerpt: ANALYTICAL TECHNIQUES FOR THE ELUCIDATION OF PROTEIN FUNCTION An essential aid for scientists seeking alternative techniques for investigating proteins Proteins are the building blocks of living organisms, and they play an enormous range of fundamental roles in sustaining and shaping life. The critical determinant of a protein’s function is its structure, and the analysis of protein structures has therefore become a significant component of biological research. In recent years, longstanding analytical techniques such as X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy have been supplemented by a number of new methods which promise to revolutionize the study of proteins and their functions. Analytical Techniques for the Elucidation of Protein Function serves as an introduction to these techniques, which are especially crucial for analyzing intrinsically disordered regions and post-translational modifications. These have revolutionized the study of proteins in recent years, and conventional methods for analyzing protein structures are no longer sufficient to work through their ramifications. This book therefore brings greater awareness of techniques which promise to produce the very cutting edge of protein research. Analytical Techniques for the Elucidation of Protein Function readers will find: A discussion of techniques including electron paramagnetic resonance (ESR) spectroscopy, neutron scattering, Raman imaging, and more Both theoretical background and practical applications for each technique Contributions from leading international researchers into protein structure and function This practically focused text is a valuable reference for protein and peptide analysis and synthesis researchers, as well as for graduate and advanced undergraduate students in the life sciences.

Download or read book Protein Interactions Computational Methods Analysis And Applications written by M Michael Gromiha and published by World Scientific. This book was released on 2020-03-05 with total page 424 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is indexed in Chemical Abstracts ServiceThe interactions of proteins with other molecules are important in many cellular activities. Investigations have been carried out to understand the recognition mechanism, identify the binding sites, analyze the the binding affinity of complexes, and study the influence of mutations on diseases. Protein interactions are also crucial in structure-based drug design.This book covers computational analysis of protein-protein, protein-nucleic acid and protein-ligand interactions and their applications. It provides up-to-date information and the latest developments from experts in the field, using illustrations to explain the key concepts and applications. This volume can serve as a single source on comparative studies of proteins interacting with proteins/DNAs/RNAs/carbohydrates and small molecules.

Download or read book Mass Spectrometry based Strategies for Protein Characterization written by Ke Li (Chemist) and published by . This book was released on 2018 with total page 189 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mass spectrometry (MS)-based protein footprinting characterizes protein structure and protein-ligand interactions by interrogating protein solvent-accessible surfaces by using chemical reagents as probes. The method is highly applicable to protein or protein-ligand complexes that are difficult to study by conventional means such as X-ray crystallography and nuclear magnetic resonance. In this dissertation, we describe the development and application of MS-based protein footprinting from three perspectives, including I) protein aggregation and amyloid formation (Chapter 2-3), II) protein-ligand interactions (Chapter 4-5), and III) in-cellulo structures and dynamic motion of membrane proteins (Chapter 6). Fast Photochemical Oxidation of Proteins (FPOP) is the main methodology implemented in the work presented in this dissertation. Chapter 1 provides an overview of FPOP and discusses its fundamentals as well as its important applications in both academic research and biotechnology drug development. In Part I, Chapter 2 covers the early method development of FPOP for monitoring amyloid beta (A[beta]) aggregation. In this work, we demonstrated the high sensitivity and spatial resolution of the method in probing the solvent accessibility of A[beta] at global, sub-regional, and some amino-acid residue levels as a function of its aggregation, and revealed A[beta] species at various oligomeric states identified by their characteristic modification levels. In Chapter 3, we extended the application of the platform to assess the effect of a putative polyphenol inhibitor on amyloid formation and to provide insights into the mechanism of action of the inhibitor in remodeling A[beta] aggregation pathways. In Part II, we evaluated different protein footprinting techniques, including FPOP, hydrogen-deuterium exchange (HDX), and carboxyl group footprinting, for probing protein-ligand (drug candidates) interaction in the context of a therapeutic development. Chapter 4 focused on protein-protein interaction by investigating the epitope of IL-6 receptor for two adnectins that have similar apparent biophysical properties. In Chapter 5, we probed the hydrophobic binding cavity of bromodomain protein for a small molecule inhibitor. This study serves as an example of interrogating protein-small molecule interactions. The two studies in Part II demonstrate the unique capabilities and limitations of protein footprinting methods in protein structural characterization. In Part III, we pushed the boundary of MS-based protein footprinting by applying the method to footprint live cells and investigate the dynamic structures/motion of membrane-transport proteins in their native cellular environment. We employed protein engineering, suspension cell expression and isotopic-encoded carboxyl group footprinting to identify salt bridges in two proteins, GLUT1 and GLUT5, that control their alternating access motions for substrate translocation. With functional analysis and mutagenesis, live-cell footprinting provides new insights into the transport mechanism of proteins in the major facilitator superfamily. The five studies in the dissertation demonstrate the powerful capability of MS-based protein footprinting in protein structural biology and biophysics research. The method also holds great potential in studying more complicated biological systems and solving demanding problems related to protein structure and properties.

Download or read book Principles of Proteomics written by Richard Twyman and published by Garland Science. This book was released on 2004-06-02 with total page 372 pages. Available in PDF, EPUB and Kindle. Book excerpt: Principles of Proteomics is designed specifically to explain the different stages of proteomic analysis, their complexities and their jargon to students and researchers in a non-technical overview of the field. The author describes the broad range of problems which proteomics can address, including structural proteomics, interaction proteomics, protein modification analysis and functional proteomics. Methodologies are described in user-friendly language, from the more traditional two-dimensional gel electrophoresis to the new developments in protein chip technologies. These are well presented in the context of overall strategies which can be adopted to address the different aspects of large-scale protein analysis.

Download or read book Advances in Protein Molecular and Structural Biology Methods written by Timir Tripathi and published by Academic Press. This book was released on 2022-01-14 with total page 716 pages. Available in PDF, EPUB and Kindle. Book excerpt: Advances in Protein Molecular and Structural Biology Methods offers a complete overview of the latest tools and methods applicable to the study of proteins at the molecular and structural level. The book begins with sections exploring tools to optimize recombinant protein expression and biophysical techniques such as fluorescence spectroscopy, NMR, mass spectrometry, cryo-electron microscopy, and X-ray crystallography. It then moves towards computational approaches, considering structural bioinformatics, molecular dynamics simulations, and deep machine learning technologies. The book also covers methods applied to intrinsically disordered proteins (IDPs)followed by chapters on protein interaction networks, protein function, and protein design and engineering. It provides researchers with an extensive toolkit of methods and techniques to draw from when conducting their own experimental work, taking them from foundational concepts to practical application. - Presents a thorough overview of the latest and emerging methods and technologies for protein study - Explores biophysical techniques, including nuclear magnetic resonance, X-ray crystallography, and cryo-electron microscopy - Includes computational and machine learning methods - Features a section dedicated to tools and techniques specific to studying intrinsically disordered proteins

Download or read book On protein structure function and modularity from an evolutionary perspective written by Robert Pilstål and published by Linköping University Electronic Press. This book was released on 2018-05-31 with total page 206 pages. Available in PDF, EPUB and Kindle. Book excerpt: We are compounded entities, given life by a complex molecular machinery. When studying these molecules we have to make sense of a diverse set of dynamical nanostructures with wast and intricate patterns of interactions. Protein polymers is one of the major groups of building blocks of such nanostructures which fold up into more or less distinct three dimensional structures. Due to their shape, dynamics and chemical properties proteins are able to perform a plethora of specific functions essential to all known cellular lifeforms. The connection between protein sequence, translated into protein structure and in the continuation into protein function is well accepted but poorly understood. Malfunction in the process of protein folding is known to be implicated in natural aging, cancer and degenerative diseases such as Alzheimer's. Protein folds are described hierarchically by structural ontologies such as SCOP, CATH and Pfam all which has yet to succeed in deciphering the natural language of protein function. These paradigmatic views centered on protein structure fail to describe more mutable entities, such as intrinsically disordered proteins (IDPs) which lack a clear defined structure. As of 2012, about two thirds of cancer patients was predicted to survive past 5 years of diagnosis. Despite this, about a third do not survive and numerous of successfully treated patients suffer from secondary conditions due to chemotherapy, surgery and the like. In order to handle cancer more efficiently we have to better understand the underlying molecular mechanisms. Elusive to standard methods of investigation, IDPs have a central role in pathology; dysfunction in IDPs are key factors in cellular system failures such as cancer, as many IDPs are hub regulators for major cell functions. These IDPs carry short conserved functional boxes, that are not described by known ontologies, which suggests the existence of a smaller entity. In an investigation of a pair of such boxes of c-MYC, a plausible structural model of its interacting with Pin1 emerged, but such a model still leaves the observer with a puzzle of understanding the actual function of that interaction. If the protein is represented as a graph and modeled as the interaction patterns instead of as a structural entity, another picture emerges. As a graph, there is a parable from that of the boxes of IDPs, to that of sectors of allosterically connected residues and the theory of foldons and folding units. Such a description is also useful in deciphering the implications of specific mutations. In order to render a functional description feasible for both structured and disordered proteins, there is a need of a model separate from form and structure. Realized as protein primes, patterns of interaction, which has a specific function that can be defined as prime interactions and context. With function defined as interactions, it might be possible that the discussion of proteins and their mechanisms is thereby simplified to the point rendering protein structural determination merely supplementary to understanding protein function. Människan byggs upp av celler, de i sin tur består av än mindre beståndsdelar; livets molekyler. Dessa fungerar som mekaniska byggstenar, likt maskiner och robotar som sliter vid fabrikens band; envar utförandes en absolut nödvändig funktion för cellens, och hela kroppens, fortsatta överlevnad. De av livets molekyler som beskrivs centralt i den här avhandling är proteiner, vilka i sin tur består utav en lång kedja, med olika typer av länkar, som likt garn lindar upp sig i ett nystan av en (mer eller mindre...) bestämd struktur som avgör dess roll och funktion i cellen. Intrinsiellt oordnade proteiner (IDP) går emot denna enkla åskådning; de är proteiner som saknar struktur och beter sig mer likt spaghetti i vatten än en maskin. IDP är ändå funktionella och bär på centrala roller i cellens maskineri; exempel är oncoproteinet c-Myc som agerar "gaspedal" för cellen - fel i c-Myc's funktion leder till att cellerna löper amok, delar sig hejdlöst och vi får cancer. Man har upptäckt att c-Myc har en ombytlig struktur vi inte kan se; studier av punktvisa förändringar, mutationer, i kedjan av byggstenar hos c-Myc visar att många länkar har viktiga roller i funktionen. Detta ger oss bättre förståelse om cancer men samtidigt är laboratoriearbetet både komplicerat och dyrt; här kan evolutionen vägleda oss och avslöja hemligheterna snabbare. Molekylär evolution studeras genom att beräkna variation i proteinkedjan mellan besläktade arter som finns lagrade i databaser; detta visar snabbt, via nätverksanalys och grafteori, vilka delar av proteinet som är centrala och kopplade till varandra av nödvändighet för artens fortlevnad. På så vis hjälper evolutionen oss att förstå proteinfunktioner via modeller baserade på proteinernas interaktioner snarare än deras struktur. Samma modeller kan nyttjas för att förstå dynamiska förlopp och skillnader mellan normala och patologiska varianter av proteiner; mutationer kan uppstå i vår arvsmassa som kan leda till sjukdom. Genom analys av proteinernas kopplingsnätverk i grafmodellerna kan man bättre förutsäga vilka mutationer som är farligare än andra. Dessutom har det visat sig att en sådan representation kan ge bättre förståelse för den normala funktionen hos ett protein än vad en proteinstruktur kan. Här introduceras även konceptet proteinprimärer, vilket är en abstrakt representation av proteiner centrerad på deras interaktiva mönster, snarare än på partikulär form och struktur. Det är en förhoppning att en sådan representation skall förenkla diskussionen anbelangande proteinfunktion så till den grad att strukturbestämmelse av proteiner, som är en mycket kostsam och tidskrävande process, till viss mån kan anses vara sekundär i betydelse jämfört med funktionellt modellerande baserat på evolutionära data extraherade ur våra sekvensdatabaser.